feat: implement persistent layered index and chunked binary format

Introduce the `obilayeredmap` specification and persistent MPHF-based index architecture for incremental multi-dataset indexing. Implement chunked binary serialization with a fixed `u8` k-mer count limit (256) and overlapping super-kmer segments. Add memory-mapped I/O and a companion `.idx` index file for allocation-free, O(1) unitig access. Update MkDocs navigation, enhance the k-mer comparison script, and add comprehensive tests for serialization, partitioning, and file I/O pipelines.

scripts/compare_kmers.py

@@ -75,7 +75,12 @@ def main():
     parser.add_argument("file_a", help="First FASTA file (reference)")
     parser.add_argument("file_b", help="Second FASTA file (to compare)")
     parser.add_argument(
-        "-k", "--kmer-size", type=int, default=31, metavar="K", help="k-mer size (default: 31)"
+        "-k",
+        "--kmer-size",
+        type=int,
+        default=31,
+        metavar="K",
+        help="k-mer size (default: 31)",
     )
     args = parser.parse_args()
 
@@ -104,6 +109,10 @@ def main():
 
     if only_a or only_b:
         print("\nSets differ.", file=sys.stderr)
+        if len(only_a) > 0 and len(only_b) <= 10:
+            print(f"\nOnly in A: {only_a}")
+        if len(only_b) > 0 and len(only_b) <= 10:
+            print(f"\nOnly in B: {only_b}")
         sys.exit(1)
     else:
         print("\nSets are identical.")